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Cryo-EM vs. X-ray Crystallography

Cryo-EM vs. X-ray Crystallography

Cryo-electron microscopy (cryo-EM) and X-ray crystallography are two essential techniques for enhancing our understanding of biological macromolecules at atomic resolution. Though distinct in methodology and application, these techniques are highly complementary, with each filling gaps left by the other. As researchers go deeper into the complex mechanisms underlying biological processes, leveraging both methods offers unparalleled insights, pushing structural biology toward new heights of discovery.

X-ray Crystallography: The Gold Standard

Historically, X-ray crystallography has been the predominant technique in structural biology. In this method, an X-ray beam passes through a crystallized sample and a diffraction pattern is created when the X-rays interact with the well-ordered crystal lattice. By analyzing the Bragg reflections in these patterns in terms of amplitudes and phases researchers can reconstruct the molecule's three-dimensional structure typically with atomic precision. The sharpness of these diffraction spots is key, directly correlating to the quality and order of the crystal. However, completeness of the reflections in each resolution zone plays another essential role in determining the final resolution of the three-dimensional structure and thus to what extent the structure can be interpreted.

However, a notable challenge is that not all biomolecules are easy to crystallize. Many biologically significant structures, such as membrane proteins or large, flexible macromolecular complexes, resist crystallization due to their dynamic nature. Also, crystallization often requires significant sample quantities and molecular engineering to stabilize flexible regions—limitations that have sparked the search for alternative methods. Furthermore, intermediary structures that can provide snapshots of important dynamic processes are extremely hard to crystallize.

Despite these hurdles, X-ray crystallography remains unsurpassed in resolving fine atomic details of well-ordered macromolecules. Its precision makes it the go-to technique for studying stable and crystallizable proteins, enzymes, and other biomolecules. Structural biologists use it to uncover mechanistic details that are crucial for drug development and understanding molecular interactions.

Cryo-Electron Microscopy: Flexibility for Non-Crystalline Samples

Cryo-EM, by contrast, doesn't require crystallization. Instead, biological samples are flash-frozen, capturing molecules in their near-native state. A high-energy electron beam is passed through these frozen samples, producing 2D projections of said molecules at various orientations. These images are then computationally assembled into a 3D map of the molecule.

Cryo-EM has surged in popularity, especially for large macromolecular complexes that are difficult or impossible to crystallize. Recent advancements in cryo-EM technology—such as improved electron detectors and image-processing algorithms—have led to what is referred to as the "resolution revolution." With cryo-EM, researchers can now achieve near-atomic resolution for even flexible or heterogeneous assemblies, such as viruses, ribosomes, and protein complexes.

One of cryo-EM's primary strengths is its ability to visualize large, multi-component structures in different conformational states. This flexibility enables scientists to capture dynamic interactions within macromolecular machines, something X-ray crystallography struggles to achieve. However, cryo-EM's resolution typically doesn't match the atomic-level precision of crystallography, particularly for smaller proteins or structures below 100 kDa.

Complementary Roles in Structural Biology

Despite their differences, cryo-EM and X-ray crystallography are not competing technologies but rather complementary tools that can work together for more complete structural insights. One of the most practical synergies between these methods is solving structures through an integrated approach.
For instance, cryo-EM can generate an initial low- to medium-resolution 3D map of a large protein complex, providing the overall architecture. X-ray crystallographic data of individual components can then be docked into the cryo-EM map, revealing high-resolution details of specific domains or subunits within the larger complex. This combined approach has been particularly valuable in studying systems that are too dynamic or heterogeneous for crystallography alone. Well before the so-called ‘resolution revolution’ this was effectively the go-to technique in the 1980s to elucidate large complexes at resolution beyond a nanometer.

Conversely, cryo-EM can assist X-ray crystallography by solving one of its most notorious hurdles—the phase problem. X-ray diffraction data capture only the intensity of the Bragg wave, but not its phase, making it impossible to resolve structures of large biomolecular complexes without a suitable means to derive these phases. Crystals of small compounds, such as paraffins, can often be solved using direct methods. These types of samples are also extremely well-suited to be solved using microED. Cryo-EM maps can provide an initial model for molecular replacement, thus enabling researchers to determine phases and solve the crystal structure at higher resolution.

Additionally, the distinct physical principles underlying the two methods—X-ray photons interacting with electron clouds in crystallography versus high-energy electrons interacting with atomic Coulomb potentials in cryo-EM—mean they provide slightly different structural information. In practice, this allows researchers to study molecules in different states or conformations, offering a more holistic view of biological structure and function.

Future Directions: Integration for Enhanced Discovery

As both cryo-EM and X-ray crystallography technologies continue to advance, the lines between them may blur further, with researchers increasingly using both techniques in tandem to solve complex structural puzzles. With cryo-EM achieving near-atomic resolution and micro-electron diffraction (microED) emerging as a method to solve crystallography-style biomolecules with very small crystals, structural biology is poised for breakthroughs that were unimaginable just a few decades ago.

JEOL has been at the forefront of this evolution, providing state-of-the-art cryo-EM systems that offer unmatched resolution and flexibility. By integrating cryo-EM with X-ray crystallography data, researchers using JEOL instruments can push the boundaries of structural biology, revealing intricate biological systems in unprecedented detail.

Ultimately, leveraging both cryo-EM and X-ray crystallography allows scientists to investigate macromolecular structures with an accuracy and completeness that no single method can achieve alone. As structural biology progresses, the combination of these complementary techniques will continue to drive innovation and discovery across the life sciences.

References & Further Reading

  • Wang HW, Wang JW. How cryo-electron microscopy and X-ray crystallography complement each other. Protein Sci. 2017 Jan;26(1):32-39. doi: 10.1002/pro.3022. Epub 2016 Sep 7. PMID: 27543495; PMCID: PMC5192981.

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    Which Techniques are Used in Lithium-Ion Battery Analysis?

    Which Techniques are Used in Lithium-Ion Battery Analysis?

    In modern technology, lithium-ion batteries (LIB) are found in many different applications, including electric cars and portable electronic devices, such as tablets and smartphones. Other purposes include aerospace and defense industries, energy storage systems, and medical devices. Lithium-ion batteries are now considered essential for many technological applications, making their analysis vital for manufacturing, enhancement, and applications. This blog post will focus on the techniques used to analyze lithium-ion batteries.

    Why Do We Analyze Lithium Ion Batteries?

    Lithium-ion batteries consist of many different components, layers, and structures that are essential for their high-performance properties. These comprise of fluids, powders, sheets, and other materials. The importance of analyzing LIBs lies in understanding their quality and reliability, which impacts their uses in various industries. Analyzing lithium-ion batteries is necessary to understand how they age, what internal changes occur, and what properties are present.

    Lithium Ion Batteries Analysis Techniques

      There is a growing demand for high-performance, durable lithium-ion batteries, especially now that their applications span multiple industries. Due to technological and scientific advances, several methods can be used to analyze lithium-ion batteries and their components. Below, we provide a brief overview of some key methods:
      • Scanning Electron Microscopy (SEM): SEM is a widely used method for studying the fine surface and internal structures and chemical properties of battery materials. It is also helpful for monitoring reactions and performance in next-generation batteries. Moreover, when coupled with a Windowless Energy Dispersive X-ray detector (EDS), this instrument is capable of observing lithium.
      • Transmission Electron Microscopy (TEM): This method helps scientists monitor the microstructural characteristics of lithium-ion batteries, including electrodes and materials, and study chemistry between battery components. 
      • Auger Microprobe (EMAS): Used to detect lithium, analyze a sample's surface and internal regions, and conduct depth profiling of positive and negative electrode materials, key components in lithium batteries. EMAS is also used to analyze chemical processes, irregularities, and surface structures of LIBs.
      • X-ray Fluorescence Spectroscopy (XRF): XRF enables the analysis of types and concentrations of elements in a sample, which includes the powder used in lithium-ion batteries. This method is used to identify contaminants and the structural composition of LIBs.

      JEOL USA: Lithium Ion Batteries

      JEOL USA offers the instruments discussed above and more for the analysis of lithium-ion batteries. By using these tools, engineers and researchers can assess the performance and safety levels of these systems, leading to the manufacture of higher-quality products.

      JEOL solutions are ideal for analyzing the performance and quality of LIBs, from manufacturing and failure analysis to research and development. The product ranges include spectrometers, microanalyzers, electron microscopes, and other scientific systems.

      Contact a member of JEOL today to learn more about the tools and techniques used in lithium-ion battery analysis.

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      Transmission Electron Microscopy: What Sets It Apart from Other Imaging Techniques?

      Transmission Electron Microscopy: What Sets It Apart from Other Imaging Techniques?

      Transmission electron microscopy (TEM) is a powerful imaging technique that directs a beam of electrons through a sample to produce high-resolution images. Compared to other imaging techniques, TEM offers unique advantages that make it a crucial tool in scientific research, particularly in materials science, nanotechnology, and biological sciences. In this blog post, we will explore the distinctive features of TEM and discuss how it differs from other microscopy techniques, such as scanning electron microscopy (SEM).

      Higher Resolution and Atomic-Scale Imaging

      One of the key advantages of TEM is its ability to achieve significantly higher resolution than light microscopes. TEM can magnify nanometer structures up to 50 million times,1 revealing atomic-level details that are essential for studying materials and biological samples.

      Unlike light microscopy, which is limited by the diffraction of visible light, TEM uses an electron beam with a much shorter wavelength. This allows TEM to visualize structures as small as a single column of atoms, which is thousands of times smaller than the resolvable objects seen in light microscopes.

      Transmitted Electrons and Analytical Capabilities

      TEM uses transmitted electrons, unlike SEM, which relies on detecting reflected or knocked-off electrons to create an image. This approach enables TEM to provide a different type of imaging and analysis, making it particularly useful for studying thin samples and materials with boundaries between different substances.2

      It is also worth mentioning that TEM is not only an imaging technique but also a powerful analytical method. It plays a crucial role in the physical, chemical, and biological sciences, allowing researchers to investigate the structure and composition of various specimens. TEM has proven invaluable in studying materials with complex microstructures, providing insights into the properties and behavior of advanced structural materials, electronic materials, and nanomaterials.

      Applications of TEM

      In materials science, TEM is a valuable solution for examining the structure of solid materials, particularly highly crystalline structures. It enables researchers to visualize the internal structures of materials, providing valuable information for designing and developing nanotechnology applications.3

      In the field of biology, TEM has been instrumental in studying the ultrastructure of biological samples. It has been used to identify antigens in biomedical samples, which supports the diagnosis of bacterial infections. TEM has also enabled a more comprehensive understanding of nanoparticle uptake, biodistribution, and interactions with subcellular structures.4 By visualizing cellular components and their associations, TEM has shed light on the dynamics between cells, bacteria, parasites, and viruses.

      JEOL and Transmission Electron Microscopy Solutions

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        When to Choose EDS Analysis Over EELS?

        When to Choose EDS Analysis Over EELS?

        In materials science and electron microscopy, choosing between energy-dispersive X-ray spectroscopy (EDS) and electron energy loss spectroscopy (EELS) can significantly impact the quality and type of data obtained. Understanding the strengths and limitations of each technique is crucial for making informed decisions. Below we delve into the key factors influencing the selection of EDS or EELS.

        Detailing EDS and EELS

        The ability to understand a material's elemental composition is a similarity that EDS analysis and EELS share. However, they are different techniques. Here is an overview of EELS and EDS:
        • EDS: When a sample and electron beam come into contact, the sample's atoms emit inner-shell electrons. These leave behind spaces that are filled by outer-shell electrons. While these electrons transition into the space, they give off energy, which are seen as X-rays. The characteristic X-rays can be attributed back to different elements. They are evaluated through an EDS detector by examining their energies
        • EELS: When an electron beam, one with its kinetic energy defined, meets a sample, inelastic scattering occurs and the electrons’ energy becomes lower. An electron spectrometer can study this energy reduction to determine the sample's make-up.

        Comparing EDS to EELs

          1. Elemental Range

          When considering elemental range, EDS and EELS have distinct preferences. EDS is generally more effective for heavier elements with atomic numbers greater than 11. This is due to the nature of X-ray emissions. They become more prominent and easier to detect as the atomic number increases. Conversely, EELS excels in detecting lighter elements, particularly those with atomic numbers less than 30. As a result, EELS is particularly suitable for studying light elements such as carbon, nitrogen, and oxygen, which are critical in organic and biological materials.

          2. Spatial Resolution

          Spatial resolution is a crucial factor, especially in nanomaterials research. EELS typically offers superior spatial resolution compared to EDS. This advantage arises from the ability of EELS to analyze fine structures and interfaces at the atomic scale. For instance, when studying the atomic arrangements in nanowires or the interfaces in thin films, EELS provides unparalleled detail that is essential for understanding material properties at the nanoscale.

          3. Chemical State Information

          EELS stands out for its ability to provide detailed information about the chemical bonding and electronic structure of elements. This capability is invaluable in fields such as materials science and semiconductor research, where understanding the chemical state and electronic transitions is crucial. EELS can reveal subtle changes in bonding and the electronic structure. Moreover, it can offer insights into the material's behavior under different conditions.

          4. Sample Thickness

          The choice between EDS and EELS is also influenced by sample thickness. EDS can handle thicker samples effectively, making it suitable for bulk materials. On the other hand, EELS requires thin specimens, typically under 100 nm, to avoid complications from multiple scattering events. This limitation makes sample preparation more challenging for EELS. However it does allow for the high-resolution analysis of thin films and nanostructures.

          5. Quantification

          For straightforward compositional analysis, EDS often has the upper hand. EDS is easier to quantify and provides reliable compositional data for bulk samples. Its user-friendly nature and robust quantification capabilities make it a go-to method for routine analysis, particularly in industrial applications where rapid and accurate results are necessary.

          6. Energy Resolution

          When it comes to energy resolution, EELS, especially with monochromated systems, surpasses EDS. The superior energy resolution of EELS helps detect fine structure details and subtle chemical changes that EDS might miss. This high energy resolution is essential for investigating electronic transitions and fine details in material spectra.

          7. Time and Expertise

          The practical aspects of time and expertise cannot be overlooked. EDS analysis is generally faster and requires less specialized expertise to interpret. This makes EDS more suitable for high-throughput applications and routine analysis where time efficiency is paramount. In contrast, EELS, with its complex data and higher resolution, often demands more time and expertise to interpret the results.

          Integrative Approach

          In practice, the choice between EDS and EELS is not always mutually exclusive. Many modern electron microscopes are equipped with both EDS and EELS capabilities. This can allow researchers to leverage the strengths of both techniques for a comprehensive analysis. For example, combining EDS for elemental mapping with EELS for detailed chemical state analysis can provide a holistic understanding of the material under investigation.

          Which Will You Try, EDS OR EELS?

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            Investigating the TEM Microscope: Principles, Advancements, and Applications

            Investigating the TEM Microscope: Principles, Advancements, and Applications

            Transmission Electron Microscopy (TEM) is a powerful microscopy technique that enables researchers to obtain detailed information about the composition and morphology of samples. Because of the high-resolution imaging it offers, TEM has become an invaluable method in scientific research across various fields. Throughout this blog post, we will look at TEM microscopes in more detail, including the principles behind their performance, advancements, and key applications.

            Principles of TEM Microscopy

            TEM is based on similar principles to a light microscope but uses electrons instead of photons. Utilizing electrons allows TEMs to obtain a much higher resolution in their imaging due to the much smaller wavelength compared to light. In a TEM, photons are replaced by electrons, and glass lenses are replaced by electromagnetic lenses. Rather than observing samples through an eyepiece, the images are viewed on a fluorescent screen or captured by a charge-coupled device (CCD) camera, which is then displayed on a computer screen.

            The sample is placed in the middle of the column, and the electrons transmitted through it pass through a series of lenses under the sample, such as projector lenses. This configuration allows for the formation of an image that provides a magnified view of the sample's internal structure.

            Advancements in TEM Microscopy

            There have been significant advancements in TEM microscopy in recent years, which have led to its current place as an invaluable instrument used in a wide range of scientific applications.

            Cryo-EM

            Cryo-EM is an easy-to-use electron microscope developed to understand the morphology and tomography of nanoparticles. It also enables the study of proteins and viruses at an atomic level without the need to fix or stain the samples, which plays a crucial role in cancer studies and drug development.1 

            In situ TEM Techniques

            In situ TEM techniques enable real-time observation of structural changes in materials at the nanoscale, which is important in characterization and material design. By producing high-resolution images, scientific experts can observe how materials change under specific loading conditions.3

            Applications of TEM Microscopy

            TEM microscopy is suitable for a range of scientific disciplines, from life sciences to semiconductor research. In this section, we look at them in more detail.

            Catalysis Research

            TEM techniques, particularly in situ TEM, are frequently used in catalysis research. They allow researchers to monitor changes to a sample during catalytic processes or synthesis. This is conducted to support the development of improved catalysts for various applications, ranging from energy production to environmental remediation.4

            Environmental Sciences

            TEM microscopy plays a vital role in environmental sciences, allowing researchers to examine water samples for contaminants and pollutants. Through obtaining images of these particles at the nanoscale, researchers gain deeper insights into their sources, compositions, and potential impacts on ecosystems.

            Life Sciences

            In the field of life sciences, TEM enables the study of cellular structures, viruses, and proteins at the nanoscale. By visualizing these biological components, researchers can gain insights into their intricate details and functionalities.

            Nanotechnology

            TEM is used to investigate the properties and structures of nanomaterials, such as quantum dots and nanowires. It allows researchers to analyze the characteristics of these materials at the atomic level, aiding in the development of innovative nanotechnological applications.

            Materials Science

            TEM microscopy is an important tool in materials science as it is used to analyze crystal structures, dislocations, and grain boundaries in various materials. This information helps researchers understand the properties and behavior of materials, supporting the development of improved materials.5

            Semiconductor Research

            TEM microscopy is widely used in semiconductor research to study layer growth, composition, and defects in semiconductor materials. The insights gained from TEM analyses contribute to the advancement of semiconductor technology, enabling the production of more efficient and reliable electronic devices.

            TEM with JEOL, USA.

            Transmission electron microscopy is a versatile and powerful microscopy technique that provides valuable insights into the inner structure of samples at the atomic level. With advancements like in situ TEM techniques and cryo-EM, TEM continues to evolve and expand its applications in various scientific disciplines.

            At JEOL, we have developed the CRYO ARM™ 300, a state-of-the-art cryo-TEM that provides high-stability hardware and software for cryo-EM using single particle analysis workflows. The system features an automated specimen exchange system, including a cooled specimen stage and cryo-storage device, enabling efficient loading, retrieval, and long-term storage of frozen-hydrated specimens. With its superior resolution, the CRYO ARM™ 300 can routinely determine structures to better than 2Å on a 300 kV microscope.

            Contact a member of JEOL today to learn more about transmission electron microscopy and its applications.

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                A Quick Guide to EDS Elemental Analysis

                A Quick Guide to EDS Elemental Analysis

                Energy Dispersive X-ray Spectroscopy (EDS or EDX) is an indispensable analytical technique employed in Scanning Electron Microscopes (SEM) for elemental analysis and chemical characterization. This method leverages the interaction of an electron beam with a sample to yield precise information about the sample’s elemental composition. Below we have created a quick guide to understanding the fundamentals and applications of EDS elemental analysis.

                Principle of Operation

                EDS analyzes characteristic X-rays emitted from samples as a result of irradiation with a high-energy source like an electron beam. These X-rays are generated from atoms within the sample as outer-orbital electrons fill vacancies in inner orbitals created by the interaction with the electron beam. The energy of each generated X-ray is unique to the orbital pair it originated from, so every element has a set of “characteristic” X-rays that can be used to identify it in an unknown substrate. EDS detectors analyze the energy of these X-rays to both identify elements and estimate their abundances in a sample.

                Capabilities

                EDS is a robust technique that can analyze nearly the entire periodic table - from Beryllium (⁴Be) to Uranium (⁹²U). Modern windowless EDS detectors are even capable of detecting Lithium (³Li). The capabilities of EDS include:
                • Qualitative Analysis: EDS can qualitatively determine the presence of elements in a sample. It does this through identifying the characteristic X-ray peaks.
                • Semi-Quantitative Analysis: By comparing the relative X-ray peak intensity of every element present in a sample, EDS provides a semi-quantitative assessment of element concentrations.
                • Elemental Mapping: EDS mapping is used to visualize the spatial distribution of elements within a sample, revealing compositional heterogeneity.

                Advantages

                EDS offers several significant advantages, making it a popular choice for elemental analysis:
                • Rapid Data Acquisition: EDS can quickly acquire data from a sample, allowing for fast multi-elemental analysis in seconds.
                • Non-Destructive: The technique is non-destructive, preserving the integrity of the sample for further analysis.
                • Ease of Use: EDS systems are easy to operate. Continuous advancements in EDS software to improve element identification and quantification makes this analysis technique approachable for users of any experience level.

                Limitations

                Despite its many benefits, EDS has certain limitations:
                • Energy Resolution: The energy resolution of EDS (~128-130 eV) is lower than other electron microscopy-based techniques that analyze characteristic X-rays, such as wavelength dispersive spectroscopy (WDS;~10 eV). While this can make it challenging to distinguish X-rays with similar energies, software peak deconvolution has dramatically reduced the effect of energy resolution on data interpretation. 
                • Detection Limits: With detection limits between 0.1 and 0.5 wt%, EDS is generally used to characterize major elements in a sample. Techniques like WDS may be more suitable for the accurate quantification of trace elements. 

                Sample Preparation

                In general, EDS requires little sample preparation. For element identification or EDS mapping, no additional preparation is required outside of that needed to image the sample via SEM. However, proper sample preparation is crucial for quantitative analysis to obtain accurate results. To acquire these results, samples should be clean, polished flat, and homogenous relative to the interaction volume of the electron beam (nm²-μm²). While non-conductive specimens can easily be characterized by EDS in low vacuum/variable pressure mode, adding a conductive coating, such as carbon, enables a more accurate quantitative analysis in high vacuum. 

                Data Interpretation

                Interpreting EDS data involves several steps:
                • Element Identification: Elements are distinguished by matching the measured characteristic X-ray peaks in the spectrum to a known database.
                • Quantification: Elemental composition is quantified by analyzing peak intensities. With standardless EDS, the relative peak intensities of every element present in the sample are compared and normalized to 100%. Alternatively, each peak intensity can be compared to a standard with a known concentration of that element to avoid the need to normalize the data and yield more accurate results. Matrix corrections are used to account for variations in X-ray yield as a function of sample composition and density.
                • Elemental Mapping and Line Scans: EDS mapping and line scans provide visual and quantitative information on the distribution of the elements in a sample, aiding in the understanding of material properties and behavior.

                Applications

                EDS is a versatile tool widely used across various scientific and industrial fields. In materials science, it helps characterize a range of materials including alloys, ceramic composites, geologic specimens, and more. From assessing the composition of minerals in natural samples to assisting with the failure analysis of batteries and semiconductors, EDS is fast, flexible, and powerful.

                Choose a Reliable SEM From JEOL USA

                Energy Dispersive X-ray Spectroscopy (EDS) is a powerful technique for elemental analysis and chemical characterization within SEMs. Its ability to rapidly identify and map elements makes it invaluable in research and industry applications. Understanding its principles, capabilities, advantages, and limitations ensures effective utilization of this technology for detailed material analysis.

                The abilities of SEMs are extensive, especially when coupled with EDS. Whether you are looking for more information on the SEM-EDS spectrum and element distributions with SEM-EDS mapping or you need to learn about what should be noted when using scanning microscopes, we, JEOL USA, are the specialists you need to uncover the answers to all of your questions. Not only can we provide you with insights about SEM-EDS through our articles, but we also have SEMs available for purchase on our website. Explore our full range of SEMs here and enhance your work with the inclusion of one of our products.

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                      What is Direct Write Lithography?

                      What is Direct Write Lithography?

                        Lithography is the catchall term used to describe the various methods of patterning substrate materials (glass, silicon, metal, etc.) It is a mainstay in microelectronics as it enables the fabrication of complex structures within integrated circuits (ICs), and is increasingly used in a range of materials engineering applications where nanoscale surface features could impinge on performance.

                        Direct write lithography, alternatively termed maskless lithography, is a related technique that can create these patterns. Unlike other lithography methods, for example photolithography, direct write lithography does not need a photomask. As a result, it is generally easier to conduct due to the reduced number of mandatory stages. It is also useful for generating repeated designs.

                        This article will provide more insights about direct write lithography.

                        Techniques in Direct Write Lithography

                        Direct write lithography encompasses various techniques and pattern etching options:
                        • Direct Laser Writing: This method uses a spatial light-modulating micro-array to form patterns on the substrate’s photoresist by controlling laser light exposure.
                        • Electron Beam Lithography (EBL): EBL generates patterns using an electron beam, offering high resolutions below 10 nanometers, making it suitable for intricate designs.
                        • Focused Ion Beam (FIB) Lithography: This technique employs a focused ion beam to etch or deposit patterns, providing precise control over the etching or deposition process.
                        • Dip Pen Nanolithography: Utilizing probe tips, this method directly deposits material onto the substrate to form patterns.
                        • Proton Beam Writing: This involves using a focused proton beam to create patterns, similar to electron and ion beam methods but with different interaction characteristics with the substrate material.

                        Process of Direct Write Lithography

                        The direct write lithography process is relatively straightforward, though each step can have many variations:
                        1. Resist Application: A substrate is coated with a resist layer.
                        2. Pattern Generation: Using computer-aided design (CAD) software, the desired pattern is defined. It is then converted to a GDSII (GDS) file containing layer information, before finally being converted into the machine language of the lithography tool. 
                        3. Exposure: The exposure system, guided by the GDS file, precisely patterns the substrate.
                        4. Rinsing: The remaining resist is rinsed off, leaving a positive (or negative) pattern for subsequent etching or deposition steps.

                        Benefits of Using Direct Write Lithography

                        Direct write lithography offers significant advantages, particularly in the area of prototyping speed. The technique eliminates the need for a photomask, allowing patterns to be altered rapidly. This facilitates quick prototyping and supports iterative design processes, making it highly efficient for developing and testing new designs. Additionally, direct write lithography techniques, such as electron beam lithography, provide high-resolution patterns with excellent definition. This ensures that the final design is accurate and detailed. The flexibility of direct write lithography is another major benefit; without a photomask, modifications to patterns can be made easily, enhancing the overall design and fabrication process.

                        Areas That Utilize Direct Write Lithography

                        Direct write lithography plays a crucial role in the semiconductor industry, where it is essential for forming detailed patterns on silicon wafers. It is also used to create photomasks for chip production and prototype studies, contributing to the development of advanced semiconductor devices. In the field of microelectromechanical systems (MEMS), direct write lithography is employed to form actuators and sensors that are vital components of these devices. The photonics industry also utilizes this technique to generate photonic crystals and waveguides, driving advancements in photonic technologies and enabling the development of innovative optical components.

                        Enhancements and Future Directions

                        To enhance the capabilities of direct write lithography, the incorporation of higher accelerating voltages could significantly improve resolution. This would enable even finer patterning and greater precision in the fabrication process. Due to an increased focus on photonics and waveguides, a new method of steering the electron beam at any angle has been developed. This yields improved line edge roughness and overall pattern fidelity, resulting in a more efficient device. Thanks to the development of these capabilities, the overall usability of direct write lithography will be increased, making it more effective for a wider array of applications and further solidifying its place in advanced manufacturing technologies.

                        Elevate Your Direct Write Lithography With Equipment From JEOL USA

                        The future seems optimistic for direct write lithography and its placement in different areas, such as photonics, nanotechnology, and the semiconductor industry, appears secure. Should you want to use it in your own work, why not look at the direct write lithography equipment we, JEOL USA, can offer?

                        Our JBX-A9 and JBX-8100FS are both e-beam direct write lithography systems. The JBX-A9 offers world class performance. It is especially ideal for an industrial setting and accepts wafers up to 300mm. For an EBL with a high throughput and greater flexibility, look to the JBX-8100FS. There are also documents listed on our website if you need additional information about direct write lithography. Let us help you select your direct write lithography technology. That way you can use excellent tools to enhance the patterns of your substrates.

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                        How to Decipher an SEM-EDS Spectrum

                        How to Decipher an SEM-EDS Spectrum

                        Investigating the chemical composition of materials is important for fully understanding their material properties. Often, chemical heterogeneity at the micro- to nanoscale influences the macroscopic behavior of materials. For these types of samples, SEM-EDS is ideal.

                        Scanning Electron Microscopy (SEM) can be used in tandem with Energy Dispersive X-ray Spectroscopy (EDS) to better understand material properties. At its core, SEM uses a high-energy electron beam to characterize samples at the micro- to nanoscale, offering higher resolution and depth of field than other microscopy techniques. Secondary and backscattered electrons generated by interactions between the electron beam and sample can be used to characterize surface morphology and composition respectively. Similarly, characteristic X-rays generated by the sample can be analyzed to assess its composition.

                        Characteristic X-rays are emitted when outer orbital electrons within an atom relax to fill lower-energy vacancies within inner orbitals created by a high-energy source such as an electron beam. Both the energy and wavelength of these X-rays are unique to the element they are generated from. While multiple techniques exist to analyze these X-rays, perhaps the most common to pair with SEM is EDS. At their core, EDS detectors analyze the chemical composition of materials by counting the X-rays being generated and measuring each X-ray’s energy to determine what element it came from.

                        EDS detectors are prized for their speed, versatility and ease of use. They allow users to quickly assess what elements are present in a sample and estimate the relative abundances, often in near-real time and without destroying the sample. We often visualize EDS data as a spectrum, showing X-ray energy vs. number of X-rays analyzed (intensity). Interpreting this spectrum and how it is transposed into chemical compositions is critical for accurately characterizing materials.

                        Although technologic advancements such as automatic element identification, peak deconvolution and quantification have vastly simplified interpreting EDS data, it is still important to understand the principles and best practices of SEM-EDS. This basic understanding empowers users to feel confident about their SEM-EDS results and consistently collect the best chemical data possible.

                        Read on to learn more detail about how to interpret and utilize an SEM-EDS spectrum.

                        1. Identifying the Elements Present

                        When irradiated by a high-energy source such as an electron beam, every element emits a set of X-rays with unique energies and wavelengths, hence, “characteristic X-rays”. Modern state-of-the-art SEM-EDS detectors can analyze X-rays ranging in energy from tens of electron volts (eV) to tens of kiloelectron volts (keV), allowing users to characterize nearly every element between Li and U. Most standard EDS systems are optimized for analyzing Be or B through U.

                        As shown in Figure 1 below, we visualize EDS data as a spectrum, plotting X-ray energy versus intensity. The peak intensity corresponds to the element’s relative abundance in the sample, while the width of each peak corresponds to the energy resolution of the EDS detector, typically 125-132 eV (FWHM at Mn-Kα).

                        Modern SEM-EDS software is designed to automatically identify X-ray peaks by comparing their shape and energy to a known database. This allows users of all skill levels to readily collect EDS data. However, for minor or trace (~0.1-5 wt%) elements, the software may be unable to distinguish the peak from the background radiation (Bremsstrahlung). In this case, users may need to manually examine the spectrum to confirm the element's presence. Similarly, some X-ray peaks overlap within the uncertainty of the method, requiring software peak deconvolution. While this method is robust for even severe peak overlaps (e.g., Ti-Ba or W-Si), users should be aware of what peak overlaps to expect for their sample to ensure they are adequately accounted for.

                        2. Quantitative Analysis

                          SEM-EDS is used both for providing qualitative information about the elements present and as a semi-quantitative analysis technique. To accurately quantify elemental concentrations, considerations such as the homogeneity, thickness, and surface topography of the sample are essential. These factors influence the accuracy of the quantitative results.

                          While there are multiple approaches for calculating the sample composition from an EDS spectrum, the simplest and most widely utilized is standardless quantitative analysis. This method compares the relative intensities of all of the identified peaks, normalizing the results to 100%. A matrix correction (e.g., ZAF, Φρz) is applied to account for variations in X-ray yield efficiency as a function of composition. For an ideal sample, this method is reproducible within ±2% to ±5% for major components.

                          Alternatively, some users may choose to calculate quantitative results using standards. In this case, the peak intensity of each element present in the sample is compared to that of a standard. A matrix correction is still applied. While this approach in principle yields more accurate quantitative results, it relies more heavily on ideal sample preparation and is far more susceptible to user error.

                          3. Sample Preparation

                          The quality of SEM-EDS analysis is highly dependent on sample preparation. The sample should be polished, flat, and homogeneous relative to the interaction volume of the electron beam to ensure accurate chemical analysis. For samples with non-uniform composition, acquiring spectra from multiple areas or acquiring a hyperspectral EDS map can help assess heterogeneity.The quality of SEM-EDS analysis is highly dependent on sample preparation. The sample should be polished, flat, and homogeneous relative to the interaction volume of the electron beam to ensure accurate chemical analysis. For samples with non-uniform composition, acquiring spectra from multiple areas or acquiring a hyperspectral EDS map can help assess heterogeneity.

                          4. Consideration of Topography

                          The topography of a sample can significantly affect SEM-EDS analysis. Rough or irregular surfaces may preferentially absorb or block X-rays, leading to errors in calculated composition. Positioning the sample to provide a direct line of sight between the region of interest is crucial and can assist in fully characterizing the sample, though quantitative results should be treated with caution.

                          5. Accelerating Voltage

                          The choice of accelerating voltage is critical for the excitation of X-ray lines of elements in the sample. A voltage 1.5 to 2 times higher than the energy of the X-ray lines from the element(s) of interest is recommended to efficiently excite the element. For unknown samples, using an accelerating voltage between 15 kV and 20 kV ensures that all elements present are identified. However, users might choose to collect EDS data at lower accelerating voltages to minimize interaction volume, especially to aid in characterization of small nano- to micro-scale features.

                          6. Hyperspectral EDS Mapping


                          ● Complex compositions

                          ● Overlapping peaks

                          ● Minor/trace elements with low peak/background ratios

                          Final Thoughts on the SEM-EDS Spectrum

                          With a basic understanding of the principles of SEM-EDS, researchers and analysts can effectively acquire and interpret robust EDS data. This can unlock valuable quantitative and qualitative insights into their samples.

                          It is crucial to consider the limitations and challenges associated with SEM-EDS analysis, including sample preparation and the potential for quantitative errors. However, with a careful approach and interpretation, SEM-EDS remains an indispensable tool in materials science and engineering for elemental analysis at the micro- to nano scale.

                          JEOL USA’s Tools Incorporate the SEM-EDS Spectrum

                          SEM-EDS analyses are fast, effective, and can help interrogate a wide range of material properties and characteristics. Understanding what EDS spectra are and how they can be used to inform qualitative and semi-quantitative chemical analysis of samples is essential for accurately interpreting and gaining the most out of this type of analysis.

                          SEM-EDS can provide powerful information about the material properties at the micro- to nanoscale. It is therefore utilized for with a variety of materials such as:

                          ● Polymers
                          ● Metals
                          ● Ceramics
                          ● Composites
                          ● Batteries
                          ● Pharmaceuticals
                          ● Rocks and minerals
                          ● Forensics
                          ● Electronics and semiconductors

                          Chemical analysis of these materials by SEM-EDS can be leveraged across industry, government and academic sectors for wide range of applications spanning from investigating the chemical composition of minerals in meteorites to fingerprinting forensic samples to developing next-generation energy storage solutions and beyond.

                          If you are looking for an innovative SEM-EDS tool or analytical technique to help you with your research, we, JEOL USA, would recommend browsing our website.


                          Ready to learn more about our Gather-X Windowless EDS? This state-of-the-art detector can help you characterize ultra-low energy characteristic X-rays that are under 1 keV, including Li-Kα. When paired with our ultrahigh resolution field emission SEM product line, this ground-breaking technique is transforming the types of materials that we can observe and study.

                          For more information on SEM-EDS analysis or the SEM-EDS spectrum, we invite you to browse through our website. Check out our blog page to learn more about elemental analysis with electron microscopes, a guide on energy dispersive spectroscopy and so much more!

                          Our technology can help you ensure that your materials have the right characteristics for their future applications. Contact us today to find the best SEM-EDS tool for you.

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